Period
2014 - 2019
Colaborators
Responsible: Raquel Pinho
PI: Dr.Elizabeth Maga, University of Californa, Davis, CA - United States
Colaborator: Dr. Lydia Garas, University of Californa, Davis, CA - United States
Colaborator: Dr. Elizabeth Maga, University of Californa, Davis, CA - United States
Colaborator: Dr. Bart Weimer, University of Californa, Davis, CA - United States
Colaborator: Dr. Carol Huang, University of Californa, Davis, CA - United States
Location
- University of California, Davis, CA - United States
Raquel Pinho’s main responsabilities
- Experiment design and project writing.
- Library construction for RNA-sequencing and DNA methylation experiments.
- RNA-seq and DNA methylation data processing in Linux.
- RNA-seq and DNA methylation data analysis using R.
- Weighted co-expression network analysis using WGCNA.
- Integration of intestinal transcriptome, hepatic metabolome and intestinal microbiota 16S data using MixOmics.
- Validation of NGS results using qPCR for relative gene expression analysis.
Description
Malnourishment is a risk factor for childhood mortality, jeopardizing the health of children by exacerbating diseases. Using a pig model of malnutrition, we analyzed the interplay between the phenotypic data displayed by the malnourished animals, the gene expression pattern along the intestinal tract, microbiota composition of the intestinal contents, and hepatic metabolite concentrations. Samples from the duodenum, jejunum, and ileum of malnourished (protein and calorie-restricted diet) and full-fed (no dietary restrictions) piglets were subjected to RNA-seq. Gene co-expression analysis and phenotypic correlations were made with WGCNA, while the integration of transcriptome with microbiota composition and the hepatic metabolite profile was done using mixOmics. Malnourishment caused changes in tissue gene expression that influenced energetic balance, cell proliferation, nutrient absorption, and response to stress. Overall, changes in gene expression could explain several of the phenotypes displayed by malnourished animals and lays the foundation for further mechanistic and intervention studies.
Data
BioProject: PRJNA823693
Publications
- PINHO, R. M.; GARAS L.C.; HUANG B.C; WEIMER B.C.; MAGA, E.A. Malnourishment affects gene expression along the length of the small intestine. Front. Nutr., 02 September 2022, Sec. Nutrigenomics https://doi.org/10.3389/fnut.2022.894640.
- PINHO, R. M. ; MAGA, E.A. DNA methylation as a regulator of intestinal gene expression. British Journal of Nutrition. 2021 Dec 14;126(11):1611-1625. doi: 10.1017/S0007114521000556.